collapse_rows example from docs fails

[RPanczak]

I'm trying to implement collapse_rows example from docs. It fails to give me correct output.

collapse_rows_dt <- data.frame(C1 = c(rep("a", 10), rep("b", 5)),
                               C2 = c(rep("c", 7), rep("d", 3), rep("c", 2), rep("d", 3)),
                               C3 = 1:15,
                               C4 = sample(c(0,1), 15, replace = TRUE))
kbl(collapse_rows_dt, align = "c") %>%
  kable_paper(full_width = F) %>%
  column_spec(1, bold = T) %>%
  collapse_rows(columns = 1:2, valign = "top")

Produces

Instead

My sessionInfo():

R version 4.0.4 (2021-02-15)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.1252 
[2] LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods  
[7] base     

other attached packages:
[1] kableExtra_1.3.4

loaded via a namespace (and not attached):
 [1] compiler_4.0.4    pillar_1.6.1      bslib_0.2.5.1    
 [4] jquerylib_0.1.4   highr_0.9         tools_4.0.4      
 [7] digest_0.6.27     jsonlite_1.7.2    evaluate_0.14    
[10] lifecycle_1.0.0   tibble_3.1.2      viridisLite_0.4.0
[13] pkgconfig_2.0.3   rlang_0.4.11      rstudioapi_0.13  
[16] xfun_0.23         httr_1.4.2        stringr_1.4.0    
[19] xml2_1.3.2        knitr_1.33        vctrs_0.3.8      
[22] sass_0.4.0        systemfonts_1.0.2 webshot_0.5.2    
[25] svglite_2.0.0     glue_1.4.2        R6_2.5.0         
[28] fansi_0.5.0       rmarkdown_2.8     magrittr_2.0.1   
[31] scales_1.1.1      htmltools_0.5.1.1 ellipsis_0.3.2   
[34] rvest_1.0.0       colorspace_2.0-1  utf8_1.2.1       
[37] stringi_1.6.2     munsell_0.5.0     crayon_1.4.1    

[florisvdh]

Exactly the same here! collapse_rows() seems to not alter its input.

This appears to be a duplicate of #596. I've added some findings there.

[askarlupka]

It's not working for me either. There was a previous issue, #595 which is closed now. But still after installing the ref # "a6af5c0", it was still not working

[jacpete]

I can confirm that this is still an issue on the version currently available on CRAN (1.3.4). I was having the same issues that led me here and looking to make a bug fix, but I think you just need to check the installation version of the package and ensure the bug fix in a6af5c0 is implemented.

install.packages('kableExtra')

library(kableExtra)
# Warning message:
# package ‘kableExtra’ was built under R version 4.0.5 

sessionInfo()
# R version 4.0.4 (2021-02-15)
# Platform: x86_64-w64-mingw32/x64 (64-bit)
# Running under: Windows 10 x64 (build 17763)
# 
# Matrix products: default
# 
# locale:
# [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
# [4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    
# 
# attached base packages:
# [1] stats     graphics  grDevices utils     datasets  methods   base     
# 
# other attached packages:
# [1] kableExtra_1.3.4
# 
# loaded via a namespace (and not attached):
# [1] rstudioapi_0.13   knitr_1.33        xml2_1.3.2        magrittr_2.0.1    rvest_1.0.0       munsell_0.5.0     viridisLite_0.4.0
# [8] colorspace_2.0-1  R6_2.5.0          rlang_0.4.11      stringr_1.4.0     httr_1.4.2        tools_4.0.4       webshot_0.5.2    
# [15] xfun_0.23         htmltools_0.5.1.1 systemfonts_1.0.2 gitcreds_0.1.1    digest_0.6.27     lifecycle_1.0.0   glue_1.4.2       
# [22] evaluate_0.14     rmarkdown_2.8     stringi_1.6.2     compiler_4.0.4    scales_1.1.1      svglite_2.0.0  

kableExtra:::collapse_rows_html
# function (kable_input, columns, valign, target) 
# {
#     kable_attrs <- attributes(kable_input)
#     kable_xml <- kable_as_xml(kable_input)
#     kable_tbody <- xml_tpart(kable_xml, "tbody")
#     kable_dt <- rvest::html_table(xml2::read_html(as.character(kable_input)))[[1]]
#     if (is.null(columns)) {
#         columns <- seq(1, ncol(kable_dt))
#     }
#     if (!is.null(target)) {
#         if (!target %in% columns) {
#             stop("target has to be within the range of columns")
#         }
#     }
#     if (!is.null(kable_attrs$header_above)) {
#         kable_dt_col_names <- unlist(kable_dt[kable_attrs$header_above, 
#         ])
#         kable_dt <- kable_dt[-(1:kable_attrs$header_above), ]
#         names(kable_dt) <- kable_dt_col_names
#     }
#     collapse_matrix <- collapse_row_matrix(kable_dt, columns, 
#                                            target = target)
#     for (i in 1:nrow(collapse_matrix)) {
#         matrix_row <- collapse_matrix[i, ]
#         names(matrix_row) <- names(collapse_matrix)
#         target_row <- xml_child(kable_tbody, i)
#         row_node_rm_count <- 0
#         for (j in 1:length(matrix_row)) {
#             collapsing_col <- as.numeric(sub("x", "", 
#                                              names(matrix_row)[j])) - row_node_rm_count
#             target_cell <- xml_child(target_row, collapsing_col)
#             if (matrix_row[j] == 0) {
#                 xml_remove(target_cell)
#                 row_node_rm_count <- row_node_rm_count + 1
#             }
#             else if (matrix_row[j] != 1) {
#                 xml_attr(target_cell, "rowspan") <- matrix_row[j]
#                 xml_attr(target_cell, "style") <- paste0(xml_attr(target_cell, 
#                                                                   "style"), "vertical-align: ", valign, 
#                                                          " !important;")
#             }
#         }
#     }
#     out <- as_kable_xml(kable_xml)
#     kable_attrs$collapse_matrix <- collapse_matrix
#     attributes(out) <- kable_attrs
#     if (!"kableExtra" %in% class(out)) 
#         class(out) <- c("kableExtra", class(out))
#     return(out)
# }
# <bytecode: 0x0000019f13ac1550>
# <environment: namespace:kableExtra>

The CRAN function is missing the fix from a6af5c0 .
When I run the example code, I get the wrong output.

collapse_rows_dt <- data.frame(C1 = c(rep("a", 10), rep("b", 5)),
                               C2 = c(rep("c", 7), rep("d", 3), rep("c", 2), rep("d", 3)),
                               C3 = 1:15,
                               C4 = sample(c(0,1), 15, replace = TRUE))
kbl(collapse_rows_dt, align = "c") %>%
    kable_paper(full_width = F) %>%
    column_spec(1, bold = T) %>%
    collapse_rows(columns = 1:2, valign = "top")

However after installing the package with the commit from GitHub as mentioned here, it does work.

remotes::install_github('haozhu233/kableExtra@a6af5c0')
library(kableExtra)
sessionInfo()
# R version 4.0.4 (2021-02-15)
# Platform: x86_64-w64-mingw32/x64 (64-bit)
# Running under: Windows 10 x64 (build 17763)
# 
# Matrix products: default
# 
# locale:
# [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
# [4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    
# 
# attached base packages:
# [1] stats     graphics  grDevices utils     datasets  methods   base     
# 
# other attached packages:
# [1] kableExtra_1.3.4.9000
# 
# loaded via a namespace (and not attached):
# [1] compiler_4.0.4    prettyunits_1.1.1 remotes_2.4.0     tools_4.0.4       digest_0.6.27     pkgbuild_1.2.0    evaluate_0.14    
# [8] lifecycle_1.0.0   viridisLite_0.4.0 rlang_0.4.11      cli_2.5.0         rstudioapi_0.13   curl_4.3.2        xfun_0.23        
# [15] withr_2.4.2       httr_1.4.2        stringr_1.4.0     knitr_1.33        xml2_1.3.2        gitcreds_0.1.1    systemfonts_1.0.2
# [22] rprojroot_2.0.2   webshot_0.5.2     svglite_2.0.0     glue_1.4.2        R6_2.5.0          processx_3.5.2    rmarkdown_2.8    
# [29] callr_3.7.0       magrittr_2.0.1    scales_1.1.1      ps_1.6.0          htmltools_0.5.1.1 rvest_1.0.0       colorspace_2.0-1 

collapse_rows_dt <- data.frame(C1 = c(rep("a", 10), rep("b", 5)),
                               C2 = c(rep("c", 7), rep("d", 3), rep("c", 2), rep("d", 3)),
                               C3 = 1:15,
                               C4 = sample(c(0,1), 15, replace = TRUE))
kbl(collapse_rows_dt, align = "c") %>%
    kable_paper(full_width = F) %>%
    column_spec(1, bold = T) %>%
    collapse_rows(columns = 1:2, valign = "top")

If you are still having issues with the development version of the package, I think the next step may be to look at the other dependencies this function relies on. {rvest} was mentioned as the cause of the change that required the bug fix in the first place. You may check the installation version of those packages. mine are:

library(rvest)
library(xml2)
sessionInfo()
# R version 4.0.4 (2021-02-15)
# Platform: x86_64-w64-mingw32/x64 (64-bit)
# Running under: Windows 10 x64 (build 17763)
# 
# Matrix products: default
# 
# locale:
# [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
# [4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    
# 
# attached base packages:
# [1] stats     graphics  grDevices utils     datasets  methods   base     
# 
# other attached packages:
# [1] xml2_1.3.2  rvest_1.0.0
# 
# loaded via a namespace (and not attached):
# [1] httr_1.4.2      compiler_4.0.4  magrittr_2.0.1  R6_2.5.0        gitcreds_0.1.1  tools_4.0.4     lifecycle_1.0.0 rlang_0.4.11 

[florisvdh]

Confirmed, thanks! It works fine with current GitHub version installed with remotes::install_github('haozhu233/kableExtra'). (Currently at commit 4c93f1a)

[florisvdh]

So this issue could be closed, or perhaps rephrased to say that the CRAN version still misses the fix.

[paulrougieux]

The current CRAN version kableExtra_1.3.4 still doesn't work for html output, the pdf version works however.

[jkylearmstrong]

Confirmed, thanks! It works fine with current GitHub version installed with remotes::install_github('haozhu233/kableExtra'). (Currently at commit 4c93f1a)

Confirmed that this is working for HTML with remotes::install_github('haozhu233/kableExtra') - however, the CRAN version is still not working.